Reactivity of amino acids and short peptide sequences: identifying bioactive compounds via DFT calculations.

Bioactive peptides are short amino acid sequences that play important roles in various physiological processes, including antioxidant and protective effects. These compounds can be obtained through protein hydrolysis and have a wide range of potential applications in a variety of areas. However, despite the potential of these compounds, more in-depth knowledge is still necessary to better understand details regarding their chemical reactivity and electronic properties. In this study, we used molecular modeling techniques to investigate the electronic structure of isolated amino acids (AA) and short peptide sequences. Details on the relative alignments between the frontier electronic levels, local chemical reactivity and donor-acceptor properties of the 20 primary amino acids and some di- and tripeptides were evaluated in the framework of the density functional theory (DFT). Our results suggest that the electronic properties of isolated amino acids can be used to interpret the reactivity of short sequences. We found that aromatic and charged amino acids, as well as Methionine, play a key role in determining the local reactivity of peptides, in agreement with experimental data. Our analyses also allowed us to identify the influence of the relative position of AA and terminations on the local reactivity of the sequences, which can guide experimental studies and help to propose/evaluate possible mechanisms of action. In summary, our data indicate that the position of active sites of polypeptides can be predicted from short sequences, providing a promising strategy for the synthesis and bioprospection of new optimized compounds.

Date fruit melanin is primarily based on (-)-epicatechin proanthocyanidin oligomers.

Plant-based melanin seems to be abundant, but it did not receive scientific attention despite its importance in plant biology and medicinal applications, e.g. photoprotection, radical scavenging, antimicrobial properties, etc. Date fruit melanin (DM) has complex, graphene-like, polymeric structure that needs characterization to understand its molecular properties and potential applications. This study provides the first investigation of the possible molecular composition of DM. High performance size-exclusion chromatography (HPSEC) suggested that DM contains oligomeric structures (569-3236 Da) and transmission electron microscopy (TEM) showed agglomeration of these structures in granules of low total porosity (10-1000 Å). Nuclear magnetic resonance (NMR) spectroscopy provided evidence for the presence of oligomeric proanthocyanidins and electron paramagnetic resonance (EPR) spectroscopy revealed a g-factor in the range 2.0034-2.005. Density functional theory (DFT) calculations suggested that the EPR signals can be associated with oligomeric proanthocyanidin structures having 4 and above molecular units of (-)-epicatechin. The discovery of edible melanin in date fruits and its characterization are expected to open a new area of research on its significance to nutritional and sensory characteristics of plant-based foods.

Antiviral Action against SARS-CoV-2 of a Synthetic Peptide Based on a Novel Defensin Present in the Transcriptome of the Fire Salamander (Salamandra salamandra).

The potential emergence of zoonotic diseases has raised significant concerns, particularly in light of the recent pandemic, emphasizing the urgent need for scientific preparedness. The bioprospection and characterization of new molecules are strategically relevant to the research and development of innovative drugs for viral and bacterial treatment and disease management. Amphibian species possess a diverse array of compounds, including antimicrobial peptides. This study identified the first bioactive peptide from Salamandra salamandra in a transcriptome analysis. The synthetic peptide sequence, which belongs to the defensin family, was characterized through MALDI TOF/TOF mass spectrometry. Molecular docking assays hypothesized the interaction between the identified peptide and the active binding site of the spike WT RBD/hACE2 complex. Although additional studies are required, the preliminary evaluation of the antiviral potential of synthetic SS-I was conducted through an in vitro cell-based SARS-CoV-2 infection assay. Additionally, the cytotoxic and hemolytic effects of the synthesized peptide were assessed. These preliminary findings highlighted the potential of SS-I as a chemical scaffold for drug development against COVID-19, hindering viral infection. The peptide demonstrated hemolytic activity while not exhibiting cytotoxicity at the antiviral concentration.

Exploring the antiviral activity of α-ketoamides compounds through electronic structure calculations: a structure-activity relationship study.

In recent years, the scientific community has worked intensively in the search and development of new drugs to suppress viral infections, such as COVID-19. In fact, a number of active compounds have been tested; however, the absence of significant structure-activity relationships hinders the production of optimized drugs. In this study, molecular modeling techniques were employed to investigate the electronic, structural and chemical reactivity properties of a set α-ketoamides whose antiviral activities have been reported in the literature, aiming to propose new promising derivatives. The local reactivity of the compounds was evaluated via condensed-to-atoms Fukui indexes and molecular electrostatic potential. Multivariate data analysis and random forests machine learning techniques were employed to correlate the antiviral properties and electronic and structural descriptors and identify relevant variables. A series of new derivatives were then proposed and evaluated via density functional theory-based calculations, and docking/molecular dynamics with the target protein of the virus. The results suggest that active derivatives present reduced reactivity towards electrophilic agents on the central core of the molecules and high reactivity on R1 ligands. Derivatives with higher predicted antiviral activities were proposed based on simple electronic descriptors, and their efficacies are reinforced by docking and molecular dynamics simulations.Communicated by Ramaswamy H. Sarma.

Natural cordiaquinones as strategies to inhibit the growth and biofilm formation of methicillin-sensitive and methicillin-resistant Staphylococcus spp.

AIMS: The aim of this study was to investigate the antibacterial and antibiofilm potential of cordiaquinones B, E, L, N, and O against different Staphylococci strains, in addition to analyzing in silico the observed effect. METHODS AND RESULTS: The minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) were determined according to CLSI guidelines. The inhibition of biofilm formation was investigated at sub-MICs. Atomic force microscopy (AFM) and density functional theory method were performed. The tested strains of Staphylococcus spp. were susceptible to cordiaquinones B, E, and L, among which cordiaquinone B exerted a bactericidal effect, confirmed by a bacterial growth curve study, against Staphylococcus saprophyticus. Cordiaquinones B and E showed lowest MBC values against S. saprophyticus. AFM revealed that cordiaquinone L reduced the mean cell size of S. saprophyticus. Cordiaquinones B and E inhibited the biofilm formation ability of S. aureus by ∼90%. The in silico analysis suggested that the antimicrobial activity of cordiaquinones is driven by their electron donation capability. CONCLUSIONS: Cordiaquinones inhibit the growth and biofilm formation (virulence factor) of both methicillin-sensitive and methicillin-resistant Staphylococci strains, indicating their antimicrobial potential.

Antioxidant and Neuroprotective Effects of the First Tryptophyllin Found in Snake Venom (Bothrops moojeni).

In this study, we report the isolation, characterization, and synthesis of the peptide BmT-2 belonging to the tryptophyllins family, isolated from the venom of the snake Bothrops moojeni. This is the first time a tryptophyllin is identified in snake venom. We tested whether BmT-2 had cytotoxic effects and antioxidant activity in a set of experiments that included both in vitro and cell-based assays. BmT-2 presented a radical scavenging activity toward ABTS• and AAPH-derived radicals. BmT-2 protected fluorescein, DNA molecules, and human red blood cells (RBCs) from free radicals generated by the thermal decomposition of AAPH. The novel tryptophyllin was not toxic in cell viability tests, where it (up to 0.4 mg/mL) did not cause hemolysis of human RBCs and did not cause significant loss of cell viability, showing a CC50 > 1.5 mM for cytotoxic effects against SK-N-BE(2) neuroblastoma cells. BmT-2 prevented the arsenite-induced upregulation of Nrf2 in Neuro-2a neuroblasts and the phorbol myristate acetate-induced overgeneration of reactive oxygen species and reactive nitrogen species in SK-N-BE(2) neuroblastoma cells. Electronic structure calculations and full atomistic reactive molecular dynamics simulations revealed the relevant contribution of aromatic residues in BmT-2 to its antioxidant properties. Our study presents a novel peptide classified into the family of the tryptophyllins, which has been reported exclusively in amphibians. Despite the promising results on its antioxidant activity and low cytotoxicity, the mechanisms of action of BmT-2 still need to be further elucidated.

Visible Light Photoelectrochemical Sensor for Dopamine: Determination Using Iron Vanadate Modified Electrode.

This study reports a facile approach for constructing low-cost and remarkable electroactivity iron vanadate (Fe-V-O) semiconductor material to be used as a photoelectrochemical sensor for dopamine detection. The structure and morphology of the iron vanadate obtained by the Successive Ionic Adsorption and Reaction process were critically characterized, and the photoelectrochemical characterization showed a high photoelectroactivity of the photoanode in visible light irradiation. Under best conditions, dopamine was detected by chronoamperometry at +0.35 V vs. Ag/AgCl, achieving two linear response ranges (between 1.21 and 30.32 µmol L-1, and between 30.32 and 72.77 µmol L-1). The limits of detection and quantification were 0.34 and 1.12 µmol L-1, respectively. Besides, the accuracy of the proposed electrode was assessed by determining dopamine in artificial cerebrospinal fluid, obtaining recovery values ranging from 98.7 to 102.4%. The selectivity was also evaluated by dopamine detection against several interferent species, demonstrating good precision and promising application for the proposed method. Furthermore, DFT-based electronic structure calculations were also conducted to help the interpretation. The dominant dopamine species were determined according to the experimental conditions, and their interaction with the iron vanadate photoanode was proposed. The improved light-induced DOP detection was likewise evaluated regarding the charge transfer process.

Neuroprotective effects on microglia and insights into the structure-activity relationship of an antioxidant peptide isolated from Pelophylax perezi.

Tryptophyllins constitute a heterogeneous group of peptides that are one of the first classes of peptides identified from amphibian's skin secretions. Here, we report the structural characterization and antioxidant properties of a novel tryptophyllin-like peptide, named PpT-2, isolated from the Iberian green frog Pelophylax perezi. The skin secretion of P. perezi was obtained by electrical stimulation and fractionated using RP-HPLC. De novo peptide sequencing was conducted using MALDI MS/MS. The primary structure of PpT-2 (FPWLLS-NH2 ) was confirmed by Edman degradation and subsequently investigated using in silico tools. PpT-2 shared physicochemical properties with other well-known antioxidants. To test PpT-2 for antioxidant activity in vitro, the peptide was synthesized by solid phase and assessed in the chemical-based ABTS and DPPH scavenging assays. Then, a flow cytometry experiment was conducted to assess PpT-2 antioxidant activity in oxidatively challenged murine microglial cells. As predicted by the in silico analyses, PpT-2 scavenged free radicals in vitro and suppressed the generation of reactive species in PMA-stimulated BV-2 microglia cells. We further explored possible bioactivities of PpT-2 against prostate cancer cells and bacteria, against which the peptide exerted a moderate antiproliferative effect and negligible antimicrobial activity. The biocompatibility of PpT-2 was evaluated in cytotoxicity assays and in vivo toxicity with Galleria mellonella. No toxicity was detected in cells treated with up to 512 µg/ml and in G. mellonella treated with up to 40 mg/kg PpT-2. This novel peptide, PpT-2, stands as a promising peptide with potential therapeutic and biotechnological applications, mainly for the treatment/prevention of neurodegenerative disorders.

Revisiting the hydroxylation phenomenon of SiO2: a study through "hard-hard" and "soft-soft" interactions.

Surface hydroxylation has been extensively studied over the years for a variety of applications, and studies involving hydroxylation of different silica surfaces are still carried out due to the interesting properties obtained from those modified surfaces. Although a number of theoretical studies have been employed to evaluate details on the hydroxylation phenomenon on silica (SiO2) surfaces, most of these studies are based on computationally expensive models commonly based on extended systems. In order to circumvent such an aspect, here we present a low-cost theoretical study on the SiO2 hydroxylation process aiming to evaluate aspects associated with water-SiO2 interaction. Details about local reactivity, chemical softness, and electrostatic potential were evaluated for SiO2 model substrates in the framework of the density functional theory (DFT) using a molecular approach. The obtained results from this new and promising approach were validated and complemented by fully atomistic reactive molecular dynamics (FARMD) simulations. Furthermore, the implemented approach proves to be a powerful tool that is not restricted to the study of hydroxylation, opening a promising route for low computational cost to analyze passivation and anchoring processes on a variety of oxide surfaces.

Effects of Mechanical Deformation on the Opto-Electronic Responses, Reactivity, and Performance of Conjugated Polymers: A DFT Study.

The development of polymers for optoelectronic applications is an important research area; however, a deeper understanding of the effects induced by mechanical deformations on their intrinsic properties is needed to expand their applicability and improve their durability. Despite the number of recent studies on the mechanochemistry of organic materials, the basic knowledge and applicability of such concepts in these materials are far from those for their inorganic counterparts. To bring light to this, here we employ molecular modeling techniques to evaluate the effects of mechanical deformations on the structural, optoelectronic, and reactivity properties of traditional semiconducting polymers, such as polyaniline (PANI), polythiophene (PT), poly (p-phenylene vinylene) (PPV), and polypyrrole (PPy). For this purpose, density functional theory (DFT)-based calculations were conducted for the distinct systems at varied stretching levels in order to identify the influence of structural deformations on the electronic structure of the systems. In general, it is noticed that the elongation process leads to an increase in electronic gaps, hypsochromic effects in the optical absorption spectrum, and small changes in local reactivities. Such changes can influence the performance of polymer-based devices, allowing us to establish significant structure deformation response relationships.

Sulfonated melanin derivatives: theoretical evaluation of local reactivities and chemical structures.

Melanins are natural macromolecules present in several organisms responsible for photoprotection, photosensitivity, ion chelation, and thermoregulation. Such materials have attracted attention due to their interesting electronic properties, which suggest their possible application in biocompatible devices. However, the low typical solubility of traditional melanins does not allow the production of good quality thin films. In this sense, soluble compounds obtained via alternative synthetic routes, for instance, via levodopa (L-DOPA) oxidation in sulfonated solvents (S-melanins), can be considered interesting technological materials. Despite this, the structural and electronic features of these compounds are not fully understood. In this context, here we present a theoretical study on the local reactivities of S-melanin building blocks to better understand possible mechanisms involved in its synthesis and propose extended structures of this material. For this purpose, condensed-to-atoms Fukui indices were evaluated in the framework of the density functional theory (DFT). The obtained results show that the different side groups present in S-melanins do not significantly influence the reactivity of the compound in relation to non-functionalized melanins, indicating that both materials can present similar macroscopic structures.

The peptide secreted at the water to land transition in a model amphibian has antioxidant effects.

In addition to the morphophysiological changes experienced by amphibians during metamorphosis, they must also deal with a different set of environmental constraints when they shift from the water to the land. We found that Pithecopus azureus secretes a single peptide ([M + H]+ = 658.38 Da) at the developmental stage that precedes the onset of terrestrial behaviour. De novo peptide and cDNA sequencing revealed that the peptide, named PaT-2, is expressed in tandem and is a member of the tryptophyllins family. In silico studies allowed us to identify the position of reactive sites and infer possible antioxidant mechanisms of the compounds. Cell-based assays confirmed the predicted antioxidant activity in mammalian microglia and neuroblast cells. The potential neuroprotective effect of PaT-2 was further corroborated in FRET-based live cell imaging assays, where the peptide prevented lipopolysaccharide-induced ROS production and glutamate release in human microglia. In summary, PaT-2 is the first peptide expressed during the ontogeny of P. azureus, right before the metamorphosing froglet leaves the aquatic environment to occupy terrestrial habitats. The antioxidant activity of PaT-2, predicted by in silico analyses and confirmed by cell-based assays, might be relevant for the protection of the skin of P. azureus adults against increased O2 levels and UV exposure on land compared with aquatic environments.

Ibuprofen-loaded biocompatible latex membrane for drug release: Characterization and molecular modeling.

The incorporation of drugs and bioactive compounds in the natural rubber latex (NRL) matrix has been an alternative for the development of transdermal release membranes. Ibuprofen (IBF) is known to be used to treat inflammatory diseases, but when administered orally, high concentrations can cause some adverse problems. In this work, the incorporation of IBF in the NRL membranes was evaluated by physical-chemical, in vitro permeation, hemocompatibility and molecular modeling assays. In addition, the in vitro release profile of IBF in acid and basic media was analyzed during 96 h. The IBF-NRL membrane exhibited the absence of intermolecular bonding that could hinder drug release and presented compatible mechanical properties for applications as a cutaneous adhesive (0.58 and 1.12 MPa to Young's modulus and rupture tension, respectively). The IBF-NRL system did not present a significant hemolysis degree (1.67%) within 24 h. The release test indicated that in the first hours of the study, 48.5% IBF was released at basic pH and 22.5% at acidic pH, which is characteristic of a burst effect. Then, a stable release profile was observed until the end of the assay, with total IBF release of 60% in alkaline medium and 50% in acidic medium. The drug permeation results indicated that the IBF-NRL membranes can be used for the local skin treatment with permeation of 3.11% of IBF. Dynamic Molecular simulations indicated a pronounced electric dipole in the ionized form of IBF, which suggests a more effective interaction with water, explaining the efficient drug release in alkaline solutions. In general, the results demonstrate that the IBF-NRL membrane has great potential for a new adhesive that can be used for the treatment of inflammatory processes and injuries.

Polythiophene derivatives as chemical sensors: a DFT study on the influence of side groups.

Conjugated polymers have been considered promising candidates for applications in chemical sensors, mainly due to their high versatility of synthesis, low cost, light weight, and suitable optoelectronic properties. In this context, polythiophene (PT) derivatives have been successfully employed. However, at the same time that the versatility of the synthesis allows the production of varied derivatives, the complexity of interactions with analytes hinders an efficient design of compounds with improved sensing properties. In the present report, electronic structure calculations were employed to identify promising PT derivatives for chemical sensor applications. Structural, optoelectronic, and reactivity properties of a set of branched PT derivatives were evaluated. Adsorption studies considering different gaseous compounds were conducted for selected systems. The results suggest that an appropriate choice of the side groups can lead to derivatives with improved sensorial properties. In particular, PT-CN derivative was identified as the most promising compound for high sensitive chemical sensors towards SO2 and NH3 analytes.

Reactivity of eumelanin building blocks: A DFT study of monomers and dimers.

Melanins are natural pigments with important biological properties and have been considered promising materials for several bio-electronic applications. In spite of it, until now there is no satisfactory understanding of the macromolecular structure of these compounds. In this work, we have employed electronic structure calculations to evaluate the local reactivity on monomeric building blocks of eumelanin and on a varied combination of these units (dimers). The reactivity studies were accomplished by Condensed-to-Atoms Fukui Indexes in a DFT approach. The results have evidenced a dominance order in the reactivity of the building units that guides the polymerization process of melanin. In addition, from the differences of the local reactivities it was possible to better understand the reactions that can take place during eumelanin synthesis and estimate how they could be influenced by experimental conditions.

The Antioxidant Peptide Salamandrin-I: First Bioactive Peptide Identified from Skin Secretion of Salamandra Genus (Salamandra salamandra).

Amphibian skin is a multifunctional organ that plays key roles in defense, breathing, and water balance. In this study, skin secretion samples of the fire salamander (Salamandra salamandra) were separated using RP-HPLC and de novo sequenced using MALDI-TOF MS/MS. Next, we used an in silico platform to screen antioxidant molecules in the framework of density functional theory. One of the identified peptides, salamandrin-I, [M + H]+ = 1406.6 Da, was selected for solid-phase synthesis; it showed free radical scavenging activity against DPPH and ABTS radicals. Salamandrin-I did not show antimicrobial activity against Gram-positive and -negative bacteria. In vitro assays using human microglia and red blood cells showed that salamandrin-I has no cytotoxicity up to the concentration of 100 µM. In addition, in vivo toxicity tests on Galleria mellonella larvae resulted in no mortality at 20 and 40 mg/kg. Antioxidant peptides derived from natural sources are increasingly attracting interest. Among several applications, these peptides, such as salamandrin-I, can be used as templates in the design of novel antioxidant molecules that may contribute to devising strategies for more effective control of neurological disease.

Polypyrrole derivatives for optoelectronic applications: a DFT study on the influence of side groups.

Conjugated organic polymers have been considered interesting materials for various technological applications, mainly due to their unique optoelectronic properties and the variety of methods employed in their synthesis. In this context, polypyrrole (PPy) derivatives have been widely employed. The great versatility of synthesis of this material allows the production of a number of derivatives with distinct properties, allowing their application in several areas. In this report, aiming to guide the design of compounds with specific features, electronic structure calculations were conducted to evaluate the influence of side groups in the structural, optical and electronic properties of PPy derivatives. The calculations were carried out for oligomeric systems in the framework of density functional theory. Preliminary benchmark studies were conducted by employing two distinct functionals for geometry optimization and evaluation of optoelectronic properties. Comparative studies of the bond length alternation, spatial and energetic distribution of the frontier orbitals, electronic gaps, exciton binding energies, optical absorption spectra and electronic density of states were conducted for each derivative and the influence of the side groups was discussed in terms of their electron donation/withdrawing properties. A set of simple rules (linear equations) was proposed for the prediction of optoelectronic properties of PPy derivatives. In particular, the results have shown that simple Hammett parameters of side groups are sufficient to enable the design of improved materials.

Reactivity of lignin subunits: the influence of dehydrogenation and formation of dimeric structures.

Lignin is one of the most abundant natural materials around the world, accounting for about a quarter of the woody tissue. In general, it is well known that these highly branched aromatic bio-polymers are formed from the polymerization of p-coumaryl, coniferyl, and sinapyl alcohols; however, the connection between these structures are still not known in detail. In this work, we have employed electronic structure calculations to investigate local reactivities and details regarding the connectivity between the basic structures of lignin (unmodified mono and dilignols as well as dehydrogenated monolignols). Condensed-to-atoms Fukui indexes, local softness and hard and soft acids and bases principle were employed in the analyses. The results allow identifying reactive sites on the lignin subunits and access details on the synthesis and degradation of this bio-material. In particular, it is possible to identify a strong influence of the dehydrogenation and monomer dimerization on the monolignols reactivities, which activate the O-C4 and C5 positions. Graphical Abstract The local reactivities of lignin subunits were evaluated via DFT calculations.

Antifungal and anti-inflammatory potential of eschweilenol C-rich fraction derived from Terminalia fagifolia Mart.

ETHNOPHARMACOLOGICAL RELEVANCE: Folk knowledge transmitted between generations allows traditional populations to maintain the use of medicinal plants for the treatment of several diseases. In this context, the species Terminalia fagifolia Mart., native to Brazil, is used for the treatment of chronic and infectious diseases. Plants rich in secondary metabolites, such as this species and their derivatives, may represent therapeutic alternatives for the treatment of diseases that reduce the quality of life of people. AIM OF THE STUDY: The aim of this study was to evaluate the antifungal and anti-inflammatory potential of aqueous fraction from ethanolic extract of T. fagifolia, with in silico study of the major compound of the fraction. MATERIAL AND METHODS: The phytochemical study of the aqueous fraction was performed by HPLC, LC/MS and NMR. The antifungal activity was evaluated against yeasts, by determination of the minimum inhibitory concentration and minimum fungicidal concentration. The effect on Candida albicans was analyzed by AFM. The antibiofilm potential against biofilms of C. albicans was also tested. The anti-inflammatory potential of the aqueous fraction was evaluated in vivo by the carrageenan-induced paw edema and peritonitis. A microglial model of LPS-induced neuroinflammation was also studied. Further insights on the activation mechanism were studied using quantum chemistry computer simulations. Toxicity was evaluated in the Galleria mellonella and human erythrocytes models. RESULTS: Eschweilenol C was identified as the major constituent of the aqueous fraction of the ethanolic extract of T. fagifolia. The aqueous fraction was active against all Candida strains used (sensitive and resistant to Fluconazole) with MICs ranging from 1000 to 0.4 µg/mL. By AFM it was possible to observe morphological alterations in treated Candida cells. The fraction significantly (p < 0.05) inhibited paw edema and decreased levels of malondialdehyde induced by carrageenan. In a microglial cell model, aqueous fraction demonstrated the ability to inhibit NF-κB after induction with lipopolysaccharide. The theoretical studies showed structural similarity between eschweilenol C and indomethacin and an excellent antioxidant potential. The aqueous fraction did not present toxicity in the studied models. CONCLUSION: The results indicate that the aqueous fraction of T. fagifolia has potential for biomedical applications with low toxicity. This finding can be attributed to the predominance of eschweilenol C in the aqueous fraction.